You are right. It has to come out. A good lumberyard can help you. You should be able to get the wood pretty close and experimenting with stain on some scrap will get you the rest of the way. I would seal the reverse side before installation too. Back-priming is one of those things everyone agrees you should do but hardly anyone ever does--I'd be surprised if the rest of the panels were back-primed. (Mine were not, and were pretty disgusting after 30+ years.)
Obviously you have to see what caused the damage. You think you have a leak someplace? Or maybe just de-lamination after being in place for over 40 years?
Good luck,
Joe
Joe
1977 28' Express
Twin 318s, raw water cooled
Ohio River